Fimex is a the File Interpolation, Manipulation, and EXtraction library for gridded geospatial data. It converts between different, extensible data formats (currently netcdf, NcML, grib1/2, metgm, wdb, and felt). It enables you to change the projection and interpolation of scalar and vector grids. It makes it possible to subset the gridded data and to extract only parts of the files. For simple usage, Fimex also comes with the command line program fimex.

Gwyddion is a modular SPM (Scanning Probe Microsope) data visualization and analysis tool. It can be used for all most frequently used data processing operations including: leveling, false color plotting, shading, filtering, denoising, data editing, integral transforms, grain analysis, profile extraction, fractal analysis, and many more. The program is primarily focused on SPM data analysis (e.g. data obtained from AFM, STM, NSOM, and similar microscopes). However, it can also be used for analyzing SEM (scaning electron microscopy) data or any other 2D data.

LaserFOAM performs simulations of laser pulses
using an adaptive split step Fourier method to
solve the generalized nonlinear Schrödinger
equation. It provides a graphical environment to
run and visualize the results.

The FOX (Free Objects for Crystallography) program is made for determining crystal structure ab initio from diffraction data (mostly powder diffraction). It is built on an object-oriented crystallographic computing library called ObjCryst++. FOX features a graphical interface, including a 3D OpenGL display of the crystal structure. It provides a versatile description of the crystal structures (such as atoms, molecules, and polyhedra). Special positions and overlapping atoms are automatically handled without any a priori knowledge.

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

PDB2PQR is a Python software package that
automates many of the common tasks of preparing
structures for continuum electrostatics
calculations, providing a platform-independent
utility for converting protein files in PDB format
to PQR format. These tasks include adding a
limited number of missing heavy atoms to
biomolecular structures, determining side-chain
pKas, placing missing hydrogens, optimizing the
protein for favorable hydrogen bonding, assigning
charge and radius parameters from a variety of
force fields.

gfit analyzes data using models. gfit lets the
user create a model for virtually any type of
system using a minimal amount of computer code. It
is particularly useful for studying various
systems in biophysics, biochemistry, and cell
biology. The interface for gfit models specifies
relationships between input and output variables
in a rule-based fashion. It provides flexibility
and allows the user to reuse same models for many
related problems.

guitarstring.py is a simulation of a guitar
string. It works by treating it as a chain of
alternating springs and mass points. It is able
to plot the oscillation of the string and to
produce a wav file.

AGM Build is a molecular builder and
conformational editor. It can be used for
interactive model preparation for molecular
dynamics simulations, including association of
atom types and partial charges. It features
geometry editing, lattice building, building of
chain molecules (e.g. proteins), chains with
predetermined conformations, and charges and atom
types according to selected Force Field.

Penacho is a simulation software that calculates and draws the gas dispersion of a smokestack in the atmosphere. It consists of a GUI to enter air conditions, an atmospheric dispersion modeling solver, and an interactive 3D graphics engine. Penacho draws the plume evolution, the particles' deposition and the pollutant concentration distribution, as an isosurface and a grid plane for each coordinate axis. Penacho exports its simulation results as a text file, VTK structured points, or CSV (suitable for spreadsheets).